Journal: Cancer Discovery
Article Title: MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
doi: 10.1158/2159-8290.CD-23-1529
Figure Lengend Snippet: MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, KLM1 (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.
Article Snippet: The YAPC, PATU8902, PATU8988T, NOMO1, HEL, SET2, RH30, OCI-AML3, and MOLM13 cell lines were purchased from the “Deutsche Sammlung von Mikroorganismen und Zellkulturen.” The KP2, T3M4, SUIT2, and KLM1 cell lines were purchased from the “Japanese Collection of Research Bioresources Cell Bank.” The COR-L311 cell line was purchased from the “European Collection of Authenticated Cell Cultures.” All human cell lines were grown in RPMI medium supplemented with 10% FBS and 1% penicillin/streptomycin (Gibco), if not otherwise indicated.
Techniques: Expressing, Quantitative Proteomics, Knock-Out, Infection, Staining, Flow Cytometry, Reporter Assay, Gene Knockout, ChIP-sequencing
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![MARK2/3 dependency in cancer is linked to the maintenance of YAP/TAZ function. A, mRNA expression differences comparing 19 MARK2/3-dependent with 12 MARK2/3-independent human cancer cell lines. Transcriptome data were obtained from the CCLE database, <t>KLM1</t> (GSE140484), and CHL1 (this article). TPM were calculated and the difference in log 2 (TPM + 1) was plotted. P values were calculated using empirical Bayes statistics (eBayes) for differential expression with Holm–Bonferroni (BH) correction. B, Heatmap of MARK2/3-dependent and MARK2/3-independent cancer cell lines showing dependence on YAP/TAZ and expression of target genes. Competition-based fitness assays in Cas9-expressing cancer cells after lentiviral knockout of indicated genes (expression of dgRNAs was linked with GFP). Heatmap color indicates the LFC of %GFP + (normalized to day 3 or 6 after infection). n = 3. C, Crystal violet stain of indicated cells following lentiviral knockout of indicated genes. Data shown are representative of three independent biological replicates. D, Flow cytometry histogram of YAP/TAZ:TEAD reporter assay in MDA-MB-231 cells, on day 9 after infection. Data are representative of three independent experiments. E, Gene set enrichment analysis (GSEA) of Cas9 + MDA-MB-231 cancer cells after MARK2+3 dKO , including normalized enrichment score (NES) and P value. F, Heatmap showing the GSEA NES for the YAP/TAZ gene signature following MARK2+3 dKO in dependent and independent cell lines. G, Heatmap of mRNA expression [log 2 (normalized count)] z -scores in Cas9 + MDA-MB-231 cells of genes significantly downregulated or upregulated upon MARK2+3 dKO . Expression values of downregulated genes ( n = 188) and upregulated genes ( n = 91) of two replicate samples after gene knockout were grouped based on unsupervised clustering. Significant differentially expressed genes were defined as adjusted P value < 10 −4 and LFC >2 or <−1. P values from Wald test (DEseq2) adjusted using BH. H, CUT&RUN density profile of YAP:TEAD4−bound, YAP/TAZ dKO -sensitive H3K27ac marked enhancer loci ( n = 7,896) after MARK2+3 dKO . Profiles shown are an average of 50 bp bins around the summit of the enhancers. I, Occupancy profiles of public chromatin immunoprecipitation sequencing (ChIP-seq; TEAD4, YAP; GSE66083) and CUT&RUN (H3K27ac) upon indicated gene knockout at YAP/TAZ target gene loci.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_9825/pmc11609825/pmc11609825__cd-23-1529fig2.jpg)
